I recently got a new saddle and noticed that sometimes the back of it will be several inches above my pony’s back when taking off to jump. How serious is this? How will it affect my pony and how can I fix it?
You should put all of these questions in your original post, no need for multiple separate ones. To answer your question, absolutely an ill fitting can affect your pony. Without photos it is hard to tell exactly what is going on with your saddle and where it is positioned… but if it fits bad it can interfere with your ponies movement and can hurt him and cause lots of issues.
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Hunter hooves, do you have a coach or trainer or reasonably horse savvy adult in your immediate life? If you have questions about saddle fit you should get an independent saddle fitter in to assess.
On the other hand if the saddle comes with the lease pony and the owners of the pony or the riding school don’t care then there is probably not much you can do other than to start your personal private list of all the things you will do better when you finally buy your own horse 
It would mean that your saddle does not fit your pony. When a saddle fits a horse correctly, it will lie on its back throughout the jump. When you ride on the flat, does it do the same thing? Can you still fit 3-4 fingers width under the gullet when he is moving? Is it fitting flat on his back (no bridging - a gap in the middle) when sitting on him without any pad? Not everyone has the luxury of having a saddle fitter out, and there are a lot of people here who have seen a lot of fitting and not fitting saddles. If you can post some photos that will help.
The saddle shouldn’t rock or pop up. Slight movement isn’t the end of the world but excessive lifting or “butt feedback” is not good. As noted above, it’s hard to tell without photos and sometimes it also needs to be observed in “active fit” as some saddles look good in the cross ties and not under movement.
It could be too wide, too curvy, not enough depth in the rear, and so on. Best to get it checked.
With Ponies, especially Meds and Smalls, many saddles are too long from pommel to cantle to accommodate the riders size and the cantle ends up right over the loin and flip up as described but the bigger problem is when the comes back down on that part of the back. Even on the flat, it’s putting pressure on the back over the loin. It’s tough if the rider is a little big for the Pony and can’t fit the little kid sized saddles.
No idea if that’s the case here or not, but if it is? Might be OK for a few rides but used on a regular basis, Pony will suffer a sore back which usually creates evasive behavior that gets blamed on Ponytude instead of the real problem.
